MT2 10.19

how do proteins get between organelles? (general answer)

"zip codes & mail carriers" - each protein has a specific AA sequence - add sequence - binding place for protein to drag particular protein to bind (can drive process) ex of "zip codes" to drive localizations 1. nuclear localization signal = type of short AA sequence (**MEMORIZE THIS!!**) - where protein - "importins" - import the protein into the nucleus! (nuclear localization signal) - binds to it in protein, pulls it into nucleus so can be active at proper localization 2. targeting peptide sequence - going into other organelles (chloroplast, mitochondrion) - AA sequence that's at the beginning of the peptide, gets cleaved off, says go to mitochondria, when gets there, gets cleaved off as protein passed into mitochondria to perform its function inside the mitochondria

Vast majority of drugs in some way affect the activity of a specific enzyme in cells

- Adderall - HIV protease inhibitor - Ibuprofen (Advil): inhibits Cox-2 enzyme (slows inflammation) (imp if have headache) - Vemurafenib: helpful with cancer (vemurafenib inhibitor sits inside b-Raf kinase enzyme) (effect: mutant form found in cancer is blocked in its enzymatic activity) - Lithium: inhibits GSK3beta enzyme

How might each of the following directly participate in creating the binding specificity of an enzyme active site? A. hydrophobic amino acid side chains B. beta-sheet regions of the polypeptide C. negatively charged amino acid side chains

- Hydroxyl group of substrate in R image = green ball in L image - Protein has active site - like a basket shape - substrate sitting inside basket shape in L - Alpha helices = blue on outside (general form) - Beta sheets = purple - Side chains projected into active site = yellow A - Branch side chain = very hydrophobic - Side chains (hydrophobic) are being projected in over the left side of the active site (driving binding & specific binding - ring on L of substrate is very hydrophobic, when gets in, hydrophobic-hydrophobic reaction is very favored) B Beta barrel: beta sheet rolled around itself to create a cylindrical form -Important in generating the shape of the active site! (little cylinder where can put substrate) - Also, side chains of secondary structure project away from the face of the secondary structure (also mechanism of pointing side chains into the middle of the active site so they can interact specifically with the specific molecule) C - Returning to the hydroxyl group! - Potential for H-bonding with hydroxyl group! Negatively charged amino acid side chain can drive the hydrogen bonding with that specific group - KEY bc difference between 2 types of molecules seen between S & R is the location of that hydroxyl group in space (put in a slightly different place) (May be positively charge AA side chains that would react favorable with the carboxyl group) - Bottom line: exquisite matching between structure of a protein active site & its substrates, such that it positions substrates & recognizes those substrates in a very specific way

IMP PRINCIPLE 1: membranes are selectively permeable - what does this mean? - what things can / can't go through the membrane? how?

- certain things can go through, certain things can't go through - plasma membrane surrounding living cells separates outside & inside of cell What can go through the membrane & how? 1. small, very nonpolar molecules (steroids, estrogen, CO2, glycerol, water - polar but small enough to go through, gasses, etc.): travel directly through the lipid bilayer! 2. larger (glucose) / charged molecules (Na+, Cl-, proteins) allowed through via protein channels / carriers! - can't go directly through because of charge / too big, but "screened" and let through selectively 3. even larger complexes (virus, bacterium) need rearrangement of membrane - too large to go directly through or enter via channels - endocytosis will happen for this

What suffix indicates an enzyme?

-ase

vesicular trafficking connects.... (6)

1) ER 2) Golgi 3) Plasma membrane / cell exterior 4) Endosomes 5) Lysosomes 6) Peroxisomes KEY POINTS 1. all proteins synthesized in the ER 2. way proteins move back & forth between different areas is a 2 way street: - move protein from ER & fuse outside (release outside) (exocytosis) - bring protein in from outside (endocytosis), take through membrane system, pass it from one thing to another, & break it down inside the cell - often broken down into their parts in the lysosome 3. synthesis of membrane proteins & secreted protein follows a L->R passage through this - **MEMORIZE!!** lipids (and membrane proteins) all synthesized in the ER membrane, and also transported through vesicles to the cell surface

how do proteins & other macromolecules get between these "rooms"? (3)

1. "zipcodes" - amino acid sequences specify where they belong - particular AA sequences in actual PRIMARY sequence of peptide that tells cell where to transport it 2. "doors" - specialized openings in membranes between organelles that allow them to pass inside the cell - ex1: nuclear pore complex - ex2: channels through ER membrane (where proteins translated actively into the ER lumen) 3. "in boxes" - vesicles carry them between/to the different organelles (the compartments)

glycolysis & ATP synthesis (overview)

1. add phosphates to hexose (use 2 ATP) 2. torsional stress on carbon bond 3. breaking into two 3C pieces "spring-loads" them for transfer of phosphate to ADP

features of PLANT cells that animal cells lack (4)

1. cell wall - generates form / shape (pushing against the cell wall / putting force on cell wall to hold plant in shape - allows it to generate large structures in a fixed position) 2. vacuole - intracellular organelle, takes majority of space - contributes to rigidity (water goes in through & accumulates in vacuole, so pushes against cell wall) - other functions also (don't go into) 3. plastids (e.g. chloroplasts) - chloroplasts can use light energy to synthesize sugars (IMP!!) 4. plasmodesmata - open tunnels that allow cells to be connected (connect neighboring plant cells, allow various macromolecules & other molecules to pass between them) - bc of cell wall, connection between cells different than in animals

2 types of inhibition

1. competitive 2. allosteric

what are the 2 important functions of cellular respiration?

1. converting sugar into usable forms of energy 2. serving as the basis for synthesis of the myriad of other molecules (amino acids, etc.) that make us what we are

2 things endergonic reactions can be driven by

1. directly coupled exergonic reactions (often involving ATP or other NTP's) (think "intermediate") - larger negative ∆G with a smaller +∆G: overall sum = negative ∆G, so reaction becomes spontaneous! 2. sequential exergonic reactions (think "concentration") (products "pull" or precursors "push") - because of equilibriums, can have sequential reactions linked together in cells such that one of them, by taking away the products / generating a high concentration of the reactants in the 2nd chemical reaction can pull/push reaction and make it become exergonic when it would've been endergonic if it had been on its own (less imp. point)

4 phases of cellular respiration

1. glycolysis 2. pyruvate oxidation 3. citric acid cycle 4. oxidative phosphorylation

3 important principles of membranes

1. membranes are selectively permeable 2. carriers function by opening up to let things from outside the cell enter the carrier, then opening up the other way to allow the thing through 3. the electrochemical gradient

features SHARED by plant + animal cells

1. nucleus (where genetic info stored & initially processed) 2. mitochondrial (metabolism) 3. plasma membrane (surrounding membrane outside the cell) 4. cytoskeleton (actin & tubulin & microtubules) 5. endomembrane system - ER (all over cell, imp in protein & lipid synthesis) - lysosome (degrades macromolecules) - golgi apparatus (modification of proteins) - peroxisomes (don't talk about much)

organisms can be classified by the source of energy & carbon bonds they utilize 1. phototrophs vs chemotrophs 2. autotrophs vs heterotrophs

1. phototrophs use sunlight, chemotrophs use chemical bonds 2. autotrophs take inorganic sources of carbon (CO2) and generate organic molecules; heterotrophs take them from the environment (organic sources of carbon)

2 types of energy

1. potential (stored/utilized) energy - chemical bond - ion differential across a membrane 2. kinetic (expressed) energy - shape change, location change - ex: breaking chemical bonds - ex: moving those ions across the membrane to lower that concentration differential conversion of potential -> kinetic energy associated with changes in object structure, shape, position, etc. (can be important when thinking about cells growing & developing)

enzyme structure

4 subunits together in quaternary structure 4 subunits intertwined tightly together at their ends catalase is a very stable enzyme in cells because 4 subunits attached tightly together in strong quaternary structure

what's an important source of free energy for cells?

6C sugars! important source of free energy in all cells for running biochemical processes important to life (making them overall exergonic)

endomembrane system

A network of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles. (connected membrane systems) IMP for proteins that get secreted / functional / etc. outside of cells

Which of the following transformations would yield products with less entropy than the starting material? A. the conversion of amino acids to a peptide B. the conversion of starch to monosaccharides C. the conversion of RNA to nucleotides D. the conversion of salt crystals to ions in an aqueous solution

A. the conversion of amino acids to a peptide WHY: all other cases, converting 1 thing into many things (many things can diffuse much more randomly than 1 thing - more disorder in many things than 1 thing); in A, taking many things to make 1 thing (so more order) - Take into account number of reactants & products when thinking about entropy!

substrate level phosphorylation: coupled reactions

ATP = spring loaded When put 3rd phosphate on it, pushing beta & gamma phosphate close together & linking with phosphodiester bond (spring loading like talk about before) Can unload a bigger spring - if unloading, more free energy comes out than goes in to loading the smaller spring, have -∆G overall, so overall exergonic (spontaneous) R: one of "bigger springs" that occurs during glycolysis -Phosphoenol pyruvate: has phosphate on it that can be transferred off -∆G that comes off is larger than what's needed to put the phosphate onto the ADP to make ATP ANALOGY: Top reaction = rider putting more energy into system needed to move vehicle up hill Second reaction = moving wheel Result = What's linking the 2 together? - One way to link the two together is by the reaction occurring inside of an ENZYME!! In its ACTIVE SITE!

ex of way to store potential energy in a cell

ATP!! (***IMP!!! MEMORIZE THIS CARD!!!***) 3 phosphates connected by phosphodiester bonds between individual phosphates - effect of making phosphates covalently linked = phosphates carry significant negative charge (bc of all oxygens carrying), and when push 2 negative things together, hard to do (same charges repel), so pushing them together means there's lots of stored potential energy in the bonds that'll be released when cleaved - potential energy stored in phosphate bonds because they don't break spontaneously!! (not likely to break spontaneously - being held together) - analogous to spring being held in coiled position (mouse trap) - KEY POINT: ATP is freely diffusible in cells - way to transport stored potential energy & use in other parts of cell; also effective way inside enzymes to transfer into other reactions

allostery

Because enzymes have shape, size & bulk, possible to not only regulate if enzyme active at active site itself (think about competitive inhibition), but also possible / evolved in bio that can change the SHAPE or ACTIVITY of an active site by changing something else on the other side of the protein (analogy: fingers change the shape of scissors) change shape i none place, generate a shape change in the other important because of regulation - in many enzymes inside cells, could be active / inactive forms - ex: could have particular modulator bind to one region of protein & turn on the protein (when M bound on right, it changes the side of the C - the active site - that fits the enzyme) (so get more active enzyme) (so when positive modulator is there, the enzyme is more active) opposite is also possible: INHIBITION! - •When modulator is negative modulator, it changes shape such that on other side of protein, far away from where its bound, such that the active site is not the right shape for fitting the substrate, so as long as the inhibitor is bound, the activity of the enzyme is much lower

if chemical bonds = way to store energy, what kind of bonds store less or more energy?

C-C and C-H bonds store MORE energy in bonds than C-O or H-O bonds! - why: less tight - takes more energy to hold together, so if they come apart, that energy is released SO organic molecules converted into inorganic molecules (converting one type of bond into another) - effect: release energy (going to lower energy state overall, so energy released as heat while converting) - energy released in reaction as making new C-O and H-O bonds if do reverse reaction (converting from inorganic to organic molecules), you're generating more C-C and C-H bonds and thus need to invest energy to convert in this direction! CO2, H2O (organic) molecules: very tight - take less energy to hold together, so if they come apart, this less amount of energy is released

catabolism vs anabolism

CATABOLISM: breaking down of organic molecules - hydrolysis reactions! (cleavage of bonds holding peptides, fats, proteins, nucleic acids, carbs, etc. tgt) - water is added, take bond apart (later will talk about breaking down of sugars to generate CO2 in water - going from organic molecule of sugar to an inorganic molecule) ANABOLISM: synthesizing / building organic molecules - condensation reactions! - water released in process in net (later talk about taking inorganic molecules & converting them into subunits - building blocks)

side chains in an active site are X because of tertiary structure; ex: cyclic-AMP

CLOSE TOGETHER tertiary & quaternary structure = shape side chains take in space RNase works better folded than unfolded bc actual side chains located in active site are often not next to each other on primary sequence of the protein (only when folded in 3D shape when particular side chains become close together, and can then be a place where a chemical reaction can be accelerated or facilitated) ex: cyclic-AMP - key point: in active site, in addition to the 3D organization, the 3D organization places specific side chains in a way such that can interact with the substrate when it comes in, the intermediate as the reaction is occurring or with releasing the final product - H-bonds , hydrophobic interactions, ionic interactions = all important in function of many different enzymes when bound & going through the transition state

analogy for how enzymes change the microenvironment: trying to change someone's mind

Convincing people is context dependent: finding the right place can save you a ton of emotional energy and make you more likely to succeed! 2 approaches: 1. Get angry, yell at them, stamp your feet (high investment of emotional energy) 2. Take them somewhere safe And talk to them quietly (lower investment of emotional energy) Second option takes less emotional energy to get the same (and often better) outcome (bc overall outcome of YES & getting to yes is independent of how get there) Enzymes work in similar way

Of the following choices, which is most likely to be a product of a catabolic reaction? A. a complex carbohydrate like cellulose B. a nucleic acid like RNA C. a motor protein like myosin D. a lipid like cholesterol E. an amino acid like tryptophan

E. an amino acid like tryptophan (if going other way, is most likely to be a product of a anabolic/catabolic reaction?)

how is ATP generated in cells?

ENDERGONIC reactions driven by directly coupled exergonic reactions, either 1. directly coupled by occurring in the same active site at the same time (think "immediate exchange") (directly coupling more exergonic reaction with production of ATP) 2. controlled dissipation of electrochemical differentials across a membrane (think "revolving door")

energy & work (def & ex)

ENERGY - def: ability to do work - ex (sources): sunlight, wind, fossil fuels, food, sugar WORK - def: capacity to move against a restriction - ex: synthesis of macromolecules (e.g. peptide); info storage (in stable way that maintains it) and transmission (to the next generation of the cell); building an electrochemical gradient (pushing ions against the gradient ti build up the electrochemical gradient)

chem rxns are context dependent - in the finding the right place transfer of chem bonds is "easy"

Easy = becomes highly facilitated - KEY for lowering overall activation energy bc lowers energy barrier of the transition state

activation energy analogy: mouse trap

Free energy change from tripping mousetrap comes from potential energy stored in spring being released (directly related to form of spring before & after trap goes off) As sitting, waiting for mouse to enter, spring doesn't release - only releases when something independent happens: something touches the cheese! Whatever it is that's acting on cheese = trip mechanism = activation energy = thing that allows the reaction to progressive

chemical reactions are dependent on X

G (Gibbs free energy) ∆G = ∆H - T∆S - G = Gibbs free energy (part of energy that could be used in a reaction) - H = enthalpy (available energy/chemical bond energy) - T = temperature (K) - S = entropy ∆G determines whether a process will occur spontaneously - if ∆G<0 (negative), the reaction is spontaneous!! - if ∆G>0 (positive), the reaction is non spontaneous!! if have -∆G (∆G<0) means that more work COMES OUT of the reaction than goes in (spontaneous = exergonic) - spontaneous = way of predicting whether something will happen in cell under biological conditions - exergonic = spontaneous, won't violate laws of thermodynamics, will occur spontaneously ∆G<0 = exergonic ∆G>0 = endergonic (will violate laws of thermodynamics! won't occur spontaneously)

The cell captures much of the free energy released from this reaction in new chemical bond formation by using linked reactions.

How link reactions to capture the free energy as it comes out of the breakdown of glucose 2 different ways (referring back to ability to link 2 things together in space & time such that a larger -∆G dissipation drives a smaller +∆G, and endergonic reaction, with an overall effect that you can generate ATP from ADP & phosphate) 1.Substrate level phosphorylation 2."cashing in" on a proton differential across a membrane (talking about electrochemical gradient)

The cell captures much of the free energy released from this reaction in new chemical bond formation by breaking the reaction into parts.

If break down process into lots of little steps where can capture energy as comes out in increments, efficiency/recovery of that energy is much more efficient! Ex: burning sugar -All energy comes out in 1 reaction, which generates 1 big burst of energy -Vs Ricketts Glen = free energy changes in cells - stepwise reductions of the free energy in the beginning molecule of glucose as its broken down into intermediates -High % energy transferred into other usable forms -KEY CONCEPT: break reactions into small controlled parts where energy can be recovered

catalase active site

If take 1 oxygen atom from 1 peroxide & hold onto it (shown in middle of image), can release a water Now have oxygen sitting there If bring in second H2O2, can pull out second oxygen, put them together, generate oxygen, generate second water, and run the reaction This context is incredibly important to generating this particular reaction! Looking at blue line - because reaction occurring inside the enzyme, the actual transition state (or energy required to go through the intermediate) is much lower than would be if tried to do it all at once with 2 molecules of hydrogen peroxide generating the 2 H2O and O2

enzyme inhibition

KEY POINT: if interaction between the substrate & the enzyme is so important for facilitating / accelerating the reaction rate, if stick something else into the active site to block that interaction, then can have a major affect on the ability of that particular enzyme molecule to inhibit a reaction Ex: protease inhibitor sitting in middle of protease active site, blocking access of the substrate into that active site Ex 2 (bottom): multiple different side chain interactions between inhibitor & active site of B-Raf kinase, such that all very specific interactions, the particular inhibitor can block this enzyme activity very specifically

"cashing in" on a proton differential across a membrane (method 2 for capturing free energy from glucose breakdown to generate ATP)

Majority of ATP in brain generated by this process! (oxidative phosphorylation) (cashing in on proton differential across a membrane) Thinking about linked reactions When protons move down gradient from one side to another at same time, force movement of large machine that drives this process

why is ATP important? give an ex.

Many processes in organisms that involve the hydrolysis / transfer of phosphate off / from an ATP to drive reactions Ex: to be able to run, need to be able to contract your muscles - Inside cells as running, processes of ATP hydrolysis is actively being linked to tings happening - L image: sliding Actin along myosin, enabling the process of muscle contraction - Small green balls = ATP coming in & going out - Converting lots of ATP -> ADP & phosphate as this process happens Where does ATP come from? Where does it generate in cells?

key points Metabolism is the set of biochemical reactions that transforms biomolecules and transfers energy. Organisms can be grouped according to their source of energy: Phototrophs obtain energy from sunlight and chemotrophs obtain energy from chemical compounds, and according to the source of carbon they use to build organic molecules: Heterotrophs obtain carbon from organic molecules, and autotrophs obtain carbon from inorganic sources, such as carbon dioxide. Catabolism is the set of reactions that break down molecules and release energy, and anabolism is the set of reactions that build molecules and require energy. Kinetic energy is energy of motion. Potential energy is stored energy; it depends on the structure of an object or its position relative to its surroundings. Chemical energy is a form of potential energy held in the bonds of molecules. The laws of thermodynamics govern energy flow in biological systems. The first law of thermodynamics states that energy cannot be created or destroyed. The second law of thermodynamics states that there is an increase in entropy in the universe over time. Chemical reactions involve the breaking and forming of bonds. Here, atoms themselves do not change, but which atoms are linked to each other changes, forming new molecules. The direction of a chemical reaction is influenced by the concentration of reactants and products. Gibbs free energy (G) is the amount of energy available to do work. Three thermodynamic parameters define a chemical reaction: Gibbs free energy (G), enthalpy (H), and entropy (S). Exergonic reactions are spontaneous (ΔG < 0) and release energy. Endergonic reactions are non-spontaneous (ΔG > 0) and require energy. The change of free energy in a chemical reaction is described by ΔG = ΔH - TΔS. In living systems, non-spontaneous reactions are often coupled to spontaneous ones The hydrolysis of ATP is an exergonic reaction that drives many endergonic reactions in a cell. .

Metabolism is the set of biochemical reactions that transforms biomolecules and transfers energy. Organisms can be grouped according to their source of energy: Phototrophs obtain energy from sunlight and chemotrophs obtain energy from chemical compounds, and according to the source of carbon they use to build organic molecules: Heterotrophs obtain carbon from organic molecules, and autotrophs obtain carbon from inorganic sources, such as carbon dioxide. Catabolism is the set of reactions that break down molecules and release energy, and anabolism is the set of reactions that build molecules and require energy. Kinetic energy is energy of motion. Potential energy is stored energy; it depends on the structure of an object or its position relative to its surroundings. Chemical energy is a form of potential energy held in the bonds of molecules. The laws of thermodynamics govern energy flow in biological systems. The first law of thermodynamics states that energy cannot be created or destroyed. The second law of thermodynamics states that there is an increase in entropy in the universe over time. Chemical reactions involve the breaking and forming of bonds. Here, atoms themselves do not change, but which atoms are linked to each other changes, forming new molecules. The direction of a chemical reaction is influenced by the concentration of reactants and products. Gibbs free energy (G) is the amount of energy available to do work. Three thermodynamic parameters define a chemical reaction: Gibbs free energy (G), enthalpy (H), and entropy (S). Exergonic reactions are spontaneous (ΔG < 0) and release energy. Endergonic reactions are non-spontaneous (ΔG > 0) and require energy. The change of free energy in a chemical reaction is described by ΔG = ΔH - TΔS. In living systems, non-spontaneous reactions are often coupled to spontaneous ones The hydrolysis of ATP is an exergonic reaction that drives many endergonic reactions in a cell. .

application of allostery (how allosteric regulation is used)

NEGATIVE FEEDBACK LOOPS!! structure of threonine & isoleucine - can get from threonine to isoleucine through multiple steps of chemical transformations KEY POINT: way isoleucine synthesized in bacterial cells = multiple intermediaries in between - if there's enough isoleucine around, don't want to go through all intermediate steps - BUT if not enough isoleucine around, want to take threonine & turn into isoleucine - this is an ex bc isoleucine can bind to a particular enzyme - threonine dehydratase - very first enzyme in this pathway (waht takes threonine & turns into P1) - when enough around, binds to enzyme & changes shape such that threonine doesn't bind & isn't converted into intermediates (so inhibiting first enzyme in pathway) - if not enough, mechanism to turn it off by no longer having isoleucine binding to the enzyme why do this: makes the system efficient!!

Are enzymes changed by the reaction?

NO! even though they're catalysts and generate a favorable context or environment for a chemical reaction, they themselves are NOT changed by it, such that it's important because the enzyme can do the same thing over & over again! (enzymes not about a pathway)

what can passive diffusion of water generate?

PRESSURE!

prokaryotes vs eukaryotes

PROKARYOTES single cellular - small cells (everything packed inside, maybe in diff locations, but all there) - lack an internal plasma membrane - DNA in nucleoid (clump of DNA attached inside, but not in a nucleus) EUKARYOTES multi-cellular - have sub-cellular regions - because have internal membranes, can separate cells into distinct regions (like rooms in a house!) - separated by presence of intracellular membrane systems

Example: non-covalent electrostatic interactions between amino acid side chains (positive charge) and oxygen (negative charge)position the substrate (hydrogen peroxide) inside the catalase active site for the transfer of oxygen to the enzyme, then to the product for release (O2)

Porphrin ring = blue surrounding the oxygen that's part of the intermediate Oxygen = sitting with iron (green) When this happens, look at HIS54 & ASN127 side chains - being projected INTO the active site where oxygen will be sitting Key point: electrostatic interaction between HIS54 & ASN127 (blue balls) and the oxygen This contributes to the favoring of the oxygen coming off the H2O2 & being held in the "basket" of charge Ex of how noncovalent electrostatic interaction between side chains & substrate can contribute to geometry & facility through which a chemical reaction occurs

pyruvate kinase

Pyruvate kinase catalyzes the two previous reactions so they happen together!! Mashed between blue & white regions = ADP phosphate or ATP & the phosphoenolpyruvate + water, or pyruvate Together so when phosphate comes off of phosphoenolpyruvate, goes right onto the ATP (see 10.5 pdf slide#21) Energy stored in new phosphate bond in the ATP! Bc. ATP freely diffusible, can move around cell (bc actual ATP in access of enzyme is relatively stable in cell - doesn't' break down spontaneously) (can move it to diff place & use for an entirely diff reaction)

enzymes alter the free energy at the transition state non-covalent bonds forming between the enzyme & substrate lower free energy to get to the transition state!

Q: Why are these energetically different? A: after substrate is binding, there's a drop (lowering) in free energy -Key aspect of how enzymes work - how change ∆G of transition state - that energy comes from formation of covalent bonds between the enzyme & substrate -Those formation of those noncovalent bonds releases energy (lowering free energy) - which is how enzymes can contribute to generate a transition state that has a lower activation energy! - KEY Point: all noncovalent interactions learned before for specificity & it's ability to make things go faster

(t/f) enzymes are extremely specific

TRUE Because of tight interaction between enzyme & its substrate / intermediates, one side effect that's been highly selected for over course of evolution is that ENZYMES = EXQUISITELY SELECTIVE! Where side chains are in space can be very discriminating in terms of what substrate you find or what product you actually produce Ex: A Mandelate racemase 2 forms of mandelate: differences = subtle - orientation is flipped (carbon tetramer bond is flipped in the S & R form) - Enzyme only accepts 1 but not the other! - Key feature of enzymes (mentioned when talked about trans fats & unsaturated fats in living organisms - made in enzyme catalyzed reactions) = exquisitely selective (don't make trans fat, only the cis) SIDE NOTE: Where picture came from: X-ray crystallography

T/F: a chemical reactions changes covalent bonds between atoms give an ex

TRUE: chemical reactions change covalent bonds between atoms ex: CO2 + H2O ->/<- H2CO3 - formation of bonds - if go in forward direction, the C-O double bond and H-O single bond in CO2 and H2O are broken, and then there's rearrangement so that there's 1 new O-H bond and one new C-O bond - this reaction is reversible (double arrrow ->/<-) - forward reaction occurs in capillaries - reverse reaction occurs in lungs what determines the direction of the reaction: concentration of CO2 & water vs carbonic acid (H2CO3) concentration - in lungs, CO2 is very low, so as blood comes in, H2CO3 is very high, SO rapidly convert H2CO3 into CO2, then exhale that CO2 - conversely, in capillaries, [CO2] is very high (biproduct of chem reactions in cells as part of metabolism), enzyme drives reaction R so CO2 + H2O -> H2CO3 (very soluble in blood stream, carried away in blood stream & red blood cells & taken to lungs) - SO depends on relative concentration of products & reactants!!

in ES complex, transition state(s) of substrate are favored a transition state is a shape/charge distribution/temporary bond that is structurally in between the substrate and the product

Talking about specific transition states! Think of energy (lower bar, lower ∆G to get there), but also shape! Specific features of active site on R that drive multistep chemical reaction on L that match together KEY POINT: transition state = shape / charge distribution / temporary bond is structurally in between the substrate & the product -it's encouraging them to take on a specific shape, distribution of charge, placement in space, that's in between the substrate & product, thereby facilitating the reaction

Explain why protein synthesis does or does not violate the second law of thermodynamics.

This observation does not violate the second law of thermodynamics. It simply means that there must be an input of energy in order to drive this reaction in a more "ordered" (lower entropy) direction. This input of energy would be part of an overall reaction that still increases the entropy of the system. The disorder in the OVERALL system increases. (for example heat release from amino acid tRNA bond breakage) (HOW: breaking bond btw tRNA & amino acid while also forming bond between amino acid & peptide chain (peptide bond), overall heat released from tRNA bond breakage bc. not all energy from bond breakage invested in making new bond, and part of it comes off as heat)

why is the brain particularly sensitive to ATP availability/energy turnover? give an ex which highlights why it's important.

WHY: Na+ K+ pump = important for nerves to function - uses tons of ATP to maintain flipping back & forth to keep differential of sodium high outside and potassium high inside - why: so when need to send an impulse, can be driven (neurons use ATP to maintain electrochemical gradients that maintain action potential & enables neurotransmission) EX: stroke - when brain cells deprived of oxygen for a short time - causes neuronal cell death - tells us oxygen is used to generate ATP because if don't have oxygen, can't generate ATP (turned over very rapidly, leads to cell death)

active transport vs facilitated diffusion

active transport: transporter shape change pushes ion from lower to higher ion concentration (takes energy!) facilitated diffusion: higher ion concentration pushes transporter shape change - when big differential, can drive transporter shape change, which can drive synthesis of something like ATP (can convert from one form of energy to another)

how are concentration differences across membranes "charged"? give an example.

actively! moving ions & molecules across membranes from lower to higher concentrations (won't happen spontaneously, requires energy input!) (not all movement is in direction of gradient - not always diffusion) ex: sodium-potassium pump (maintains resting potential of neurons) (primary active transport) - in resting neuron, high [Na+] outside cellular membrane, high [K+] inside - maintained by pumping K+ into cell & Na+ out of cell - this requires energy (ATP) - active process!! - KEY POINT(!!!): works through tipping carrier proteins, but the tipping is driven by 1) taking ATP & putting phosphate on the protein (1 to 2): this drives the tip (pushes ion across channel across the gradient) (energy from change in conformation of protein) 2) take phosphate off channel protein, flips back from 3 to 4 - can push against gradient - conformational change = energetically favorable - same principle, but it's the change in confirmation of protein that's pushing the movement of the atom/molecule across the gradient, rather than conc. (high -> low) across the gradient! (DIAGRAM ON 9.28 pdf #12 is very imp!! understand this)

metabolism (broad definition)

all of the chemical processes (often linked) and energy conversions (also linked) that occur in cells

energy transfers are not fully efficient, "lost" part increases entropy

analogy: go back & forth between messy room (happens by itself), invest work to put it back in order (takes work to maintain order!) **KEY CONCEPT!!!** inside body (full of highly ordered structures), way maintain these ordered structures while not violating 2nd law of thermodynamics is that product of reactions that're occurring are coming off continuously as heat (heat coming off all the time of living organisms! way reactions can occur without violating the 2nd law of thermodynamics!)

cells are the _____ ______ _______ of life. why?

basic building blocks why: - generate an environment distinct (diff) from outside (environment controlled by membranes!) - cell = place to store info for replication - ALSO place to store & use energy in a way that's non-random!

if many macromolecules in the cell are made by energetically unfavorable reactions (ex = condensation reaction), how are so many endergonic (∆G>0, non-spontaneous) reactions possible?

biological systems link chemical reactions!! so both reactions happen together when 2 things linked together in some form, the sum of the 2 reactions controls whether or not its overall spontaneous or not! ex: bicycle wheel by itself can't go uphill, but when wheel linked by chain to foot, able to move uphill how relates to bio: linking 2 things together - larger -∆G with a smaller +∆G: overall sum = negative number &reaction becomes spontaneous (KEY!!!) fundamental way enzymes work - endergonic reactions inside enzymes can be directly coupled to exergonic reactions that're more exergonic than is endergonic - HOW happens: ATP / other nucleotide triphosphates can be modified at same time as another chemical's reaction is happening in the same place - part of energy from 1 is transmitted into driving the other part become possible (in same way leg is making the wheel roll uphill) (bicycle chain links the rider to the wheel)

enzymes are able to X and Y (in terms of why "big" is better for molecules)

bring stuff together and make stuff happen

how do molecules get through the membranes? what are 2 types of transmembrane proteins? ex of a particle that travels via protein carrier.

by facilitated diffusion (high relative concentration to low) (passive) 2 types of transmembrane proteins 1. channel protein - make a pore through the membrane (embedded in membrane with hole down middle where something can pass through) - water can be transported through membrane - in general, water concentration kept in balance by passive transport through aquaporin channel protein - facilitated diffusion where going from relatively high -> low conc. = passive 2. carrier protein: tip back & forth (talked about earlier) - ex: glucose - cells normally have high need for continual supply of glucose in body from diet - continuously in cells, maintain very low conc. of glucose - when glucose enters, modified so overall [glucose] inside cell is low, so conc. outside > conc. inside, which pushes the glucose into the cells through the carrier channels

IMP PRINCIPLE 2: membranes & how carriers function - what are the 3 things it can do?

carriers will open up to let things from outside the cell enter the carrier, then will open up the other way to allow the thing through (hands tgt then flipping to elbows tgt demo) WHAT CAN DO: 1. equalize differences across a membrane (allows molecules to diffuse across membrane to equalize concentration across the membrane) 2. Take large differential - by dissipating that differential hook in a way with something that works, can accomplish something useful (by pushing through this) (by flipping back & forth, can push the thing into 2 different conformations) (can use this to make ATP, another gradient / ion / charged molecule etc.) - pushing through membrane drives something else (dissipate bigger difference across a membrane AND do work - accomplish something useful like making ATP or another gradient!!) 3. exacerbate difference across a membrane (pumping against gradient): can use something else to push against the gradient!! (exacerbate difference - reverse of 2): bind where lots, flip into other conservation & push ion against gradient across the membrane

glucose catabolism in cells captures much of the free energy release in new chemical bond formation inside cells

catabolism: break down of chemical bonds process of taking glucose molecule (C6H12O6): - has an overall structure - together with 6O2, generate 6CO2 and 6H2O - overall reaction generates a lot of free energy release! (free energy release is highly negative in the reaction) (burning carbs / sugars / hydrocarbons: release of energy quite extreme - comes in form of heat!) - different in cell: generates heat, but ALSO wide variety of molecules that can be reutilized in the transfer of energy into other chemical reactions - overall ability to do work by burning/breaking down 1 molecule of glucose yields about 32ATP net gain (so overall ∆G - 34% of that energy - is converted into usable energy - this is quite efficient due to others!)

cells & ATP hydrolysis

cells use LOTS of energy to do work all the time ATP hydrolysis = measurement of energy turnover - removal of 3rd phosphate from an ATP to generate ADP - a currency of energy - in a resting human, 3 mol ATP turned over per hour (weighs about 4 lbs) (and this is just at rest!) - this is 10x more when exercising! (bc muscles use / require a lot of energy to do work) - ATP = turned over all the time - half-life of ATP in cells = seconds (every molecule turned over within seconds of being made in brain) to minutes (for less metabolically active cells); SO lots of energy being used to do work all the time in living organisms

enzymes

certain type of protein that accelerate rate of chemical reactions in cells they are important! in terms of metabolism, reactions are being controlled & regulated by enzymes also important in medicine: - protease for HIV - if have way to block enzyme, can help block viral infection - inhibitor = structure sitting in active site of enzyme

osmotic pressure (def, how can be problematic & how cells cope - 4)

def: the pressure which needs to be applied to a solution to prevent the inward flow of water across a semipermeable membrane cells maintain high solute concentrations - if increase solute conc., simultaneously decreasing water conc. pressure generated by water can sometimes be problematic HOW CELLS COPE - motive force of water to go from liquid in blood to the cell - as water flows in (hypotonic), will make cell swell & lyse (blow up) (if conc. of water is lower, hypertonic - tend to shrink): keep conc. of solutes in blood stream such that in normal range such that normal passage of water back & forth is equal (to maintain its shape) - not only way - isotonic conditions: regulate solute conc. outside of cells so maintain a particular shape - other way to happen: put polysaccharide cell wall outside of membrane so can't expand, even though water pushing on it to expand! (common in plants, fungi, bacteria, etc.) (when plants not watered enough, lose shape bc use water pushing against the cell wall to maintain turgor - the cell pushing hard against each other to hold the leaf/plant in its shape, so not enough water lowers motive force, causing it to wilt)

2nd law of thermodynamics (and entropy)

disorder in universe is continually increasing (entropy always increasing) (entropy = measure of disorder) (SO overall in a system, entropy is increasing) (order is unlikely)

selectively permeable cellular membranes enable forming and using X gradients & 2 ways to use these gradients

electrochemical gradients (electro = charge, chemical = number) can be used 2 diff ways: 1. take usable energy & push ions (charge against charge, number against number) 2. release / generate other forms of usable energy by pushing ions in opposite direction / other way (& decrease conc. along gradient) (can drive a motor - use it to generate other forms of energy)

oxidative phosphorylation (overview)

electron carriers donate electrons to the transport chain, leading to the synthesis of ATP

how do proteins get between organelles? ("in boxes")

endomembrane enclosed lumen: connected by vesicular transport - can move things by making a vesicle that can travel from one place to another, then release its contents into another area ex: insulin is first synthesized as proinsulin, but then gets cleaved into fully active insulin once taken outside of the cell translation of any secreted protein is into the ER through the channels - proinsulin made in ER, then it's transported into the Golgi apparatus, endosomes, or by process of exocytosis (fusing outward) to release it directly outside of the cell into the outside part (what happens with proinsulin & wide variety of other proteins that are secreted) - in addition, proteins in membrane itself are produced in the membrane of the ER, transported by vesicle to the plasma membrane, then as the vesicle fuses, it puts the actual transmembrane protein right into the plasma membrane

secreted proteins & membrane proteins are synthesized right into the X Y

endoplasmic reticulum important for all types of proteins that are secreted from the cell (go out of cell - like insulin into the blood stream, then membrane proteins - transmembrane - synthesized right into the ER) actual ribosomes always located in cytoplasm, but something else happens! when ribosome starts to translate a specific peptide that has signal on it that tells the cellular machinery it belongs in the ER, the ribosome as it's translating gets attached to ER membrane through a channel that's made through a membrane, protein is translated directly through the membrane into the ER - proteins that are going to be in the nucleus / cytoplasm / mitochondria / etc. are translated by ribosomes free in the cytoplasm - proteins that are going to be in membranes / going to be excreted from the cell / etc. are going to be in other specific organelles (like lysosomes) are translated through the ER membrane right into the lumen / inside the ER signal sequence targets machinery to pull it over so ribosome attaches to ER - generates bumps on ER - the rough ER - bumps = ribosomes that are translating into the inside / lumen through the channel into the lumen of the ER or membrane of the ER if it's a transmembrane protein (where it's then localized) ("signal sequence" in growing peptide chain sends translating ribosome to channel on surface of ER membrane)

first law of thermodynamics

energy is neither lost nor gained - it just changes form - ex: sunlight = energy coming in, a lot converted to heat (a different form of energy!)

key point to know about enzymes!

enzymes accelerate the rate of how fast things happen (reactions!) measuring conversion of substrate (H2O2) into a product (O2) without enzyme, slow reaction with enzyme, faster reaction rate (substrate conc. drops rapidly & simultaneous conversion into product - can see in terms of oxygen air bubbles form when do lab experiment) *NOTE: some enzymes can change the rate of reactions by astronomical amounts - ex: catalase! (15-50 mil turnovers of substrate into product / sec for each individual molecule of catalase) (can change rate of reaction from super slow to quite fast)

how enzymes work

enzymes also make it easy for reactions to occur by generating one or more transition states in a tiny microenvironment controlled by the enzyme (an active site!) (so enzymes make it easy by generating transition states at their active sites)

enzymes are proteins that X by Y

enzymes are proteins that "make stuff happen" by enabling chemical reactions to happen faster ex: catalase enzyme - oxygen radicals are mutagenic by products of metabolism that are tightly associated with cancer & other diseases Oxygen radicals = biproduct of metabolic reactions (like what happens in electron transport chain or during photosynthesis) = very reactive & destructive, highly mutagenic, so inactivating them = important function inside cells (the reactive oxygen species known to play important roles in development of cancer + other diseases) Chemical rnx: 2H2O2 -> 2H2O + O2 Enzyme steps in: 2 step process where 1. Oxygen radicals generated inside cells can then be converted into hydrogen peroxide by superoxide dismutase 2. This hydrogen peroxide in all organisms is converted rapidly into water & oxygen by catalase (highly conserved in wide variety of organisms, including carrots)

another key point of enzymes

enzymes can generate reaction INTERMEDIATES (can have one or many) - function: lower the activation energy - amount of ∆G in overall reaction is same, BUT amount of energy needed to put in to go through the transition state is changing - the lower the amount of free energy needed to put in to go through the transition state, the faster (and more likely) the reaction is catalase connection: catalase takes a reaction that has a higher barrier in terms of activation energy & through acting on the actual molecules involved in the chemical reactions, lowers the energy barrier such that the reaction becomes very likely & goes really fast (about RATE, not outcome)

substrate level phosphorylation (method 1 for capturing free energy from glucose breakdown)

essentially generating ATP inside an enzyme net outcome of substrate phosphorylation: take ADP & phosphate, and generate an ATP out of that reaction 2 places where ATP is generated via substrate level phosphorylation: 1. glycolysis - generation of 4 ATP's - BUT requires 2 ATP to start the process, so really a net of 2 ATP comes out of this 2. citric acid cycle (occurs in mitochondrion) - generates net of 2 ATP equivalents per glucose molecule (technically GTP, but can convert to ATP, so 2 ATP equivalents)

pyruvate oxidation (overview)

fatty acids, amino acids broken down into acetyl-coA pyruvate broken down into CO2 and acetyl-CoA

citric acid cycle (overview)

fuel molecules are fully broken down, producing ATP and electron carriers

glycolysis & ATP synthesis (DETAILS)

fundamentally, the process of breaking down glucose involves putting it into a form that it becomes very unstable & breaks down 1. when glucose inside cells, succession of 2 diff enzymes, kinases, add 2 phosphates onto the glucose, generating a molecule with 2 phosphates on it in the 6C sugar, converting it into fructose-16 bisphosphate 2. effect: in first phase of glycolysis, put things on it (made molecule under lots of torsional stress) because of 2 phosphates being there (have invested free energy into generating molecule of fructose - 6C sugar - that's very unstable - so when it breaks down, its sprung loaded into generating transfer of energy in 2 diff ways) a) when break down, breaks into two 3C sugars, each with a phosphate on it b) those molecules then have free energy to transfer an electron out & add on another phosphate (generating 2 biphosphate sugars - 3C sugars with 2 phosphates on each of them, so have total of 4 phosphates loaded onto 3C sugars) - these are also very unstable! - Those 2 compounds are what can generate first 1 ATP by transferring one phosphate onto an ADP (part 1) - Then put 2 phosphate bonds in at top, transferred from 2 ATPs, and generate 4 ATPs coming out at bottom (all 4 of phosphates can be transferred onto ADP in a way that generates ATP) (part 2)

glycolysis (overview)

glucose broken down, producing ATP & electron carrier pyruvate

competitive inhibition

have a molecule (often small molecule) that enters the active site & binds there. By binding in there, it blocks the ability of the substrate to bind/get in there. this is competitive because under one scenario, substrate is bounded & reaction goes forward, OR inhibitor is bounded & substrate doesn't fit, so reaction doesn't go forward - this is a concentration thing - if have substrate / inhibitor in there, having high [substrate] rel. to [inhibitor] favors substrate, while having high [inhibitor] relative to [substrate] favors inhibitor binding - SO can overcome this by increasing [substrate] - (why can't use inhibitor of B-Raf kinase alone / on its own bc the call can then make more & more of the substrate & overcome the particular inhibition)

in glycolysis and respiration, a major outcome is X, an Y reaction

in glycolysis and respiration, a major outcome is SYNTHESIS OF ATP, an ENDERGONIC reaction How do we recover this? Intrinsic endergonic reaction Ability to take waterfall & turn into another form of energy (like in waterwheel on R) is another key concept!

Golgi apparatus (what/function & ex)

intermediate modification center for proteins and lipids (full of synthetic enzymes) ex: place where extracellular oriented / localized proteins have carbohydrates added on to them - carb trees on outside of trees put on by the enzymes / proteins that can add carbs inside the Golgi apparatus (major function of the Golgi!)

Does a chemical reaction generate energy to do work (is it energetically spontaneous)?

it can be - it depends!! Energy in system (enthalpy) = Gibbs free energy + entropy*temperature H = G + S*T part of a reaction comes as heat (increases movement of molecules) heat = definition for molecular motion (more heat, more random) change invested to do work (generates peptide bond) energy in system (enthalpy) = capacity to do work (Gibbs free energy, G) + entropy*Temp in a reaction, how does each value change? subtract (∆) -∆G = ∆H-T∆S really care about ability to do work & how much energy will come out to do work (what'll happen if something changes?)

ex of chemical reactions being dependent on G

macromolecular synthesis (forming a peptide) = forming chemical bonds (investing energy into fomration of chemical bonds) - SO +∆H is positive - at the same time, decreasing entropy (-∆S) - overall, both positive and so have an endergonic reaction! SO this is anabolism!! if breaking apart macromolecule (breaking down peptide into collection of amino acids) - catabolism = exergonic - more disorder / entropy (increasing # of molecules), so mag of S is larger - no chemical energy in peptide bonds, so H is smaller!

metabolism & ATP hydrolysis

metabolism: measurement of changes of covalent chemical bonds in energy flux across membranes that occurs in cells ATP hydrolysis means constant flux in energy & in attachments within molecules (chemical bonds) in living organisms - constant attachment of making & breaking chemical bonds within molecules of living organisms - ATP hydrolysis (conversion of ATP to ADP and P_i) lowers the potential energy (changing energy state & molecules) - this is essentially metabolism (see definition above)

life requires a constant input of energy. why?

need energy to generate order! have highly ordered processes within us to help us live! lots of nonrandom order associated with plants, viruses, ability to move in cells, etc. highly spontaneous set of events ∆G is maintained in living organisms as they're live such that they're spontaneous (∆G<0) if reach equilibrium (∆G=0), you're dead how does this occur? sugar = important in driving this process!

activation energy

need to put energy in to get a reaction started, and then potentially after reaction starts, it can run to completion first type of free energy change = ∆G overall second type of free energy change = activation energy *KEY POINT: need to invest energy in to reach a higher energy state before the reaction proceeds - activation energy can vary in how the reaction actually occurs

transition state

point in reaction where energy state is highest (highest bar to go over energetically speaking) - amount of free energy stays the same (regardless of if enzyme present or not) (reaction rate) - in principle, could make mouse trap easier / harder to trip, but exact same spring is in there - same for chemical reactions: transition state (free energy necessary to go through the transition state) can be highly variable, but enzymes that catalyze reactions LOWER the energy of the transition state such that the reaction occurs more rapidly! - speed with which trap tripped has nothing to do with the spring - it's effectively how hard you push the actual cheese to make it go off

primary vs secondary active transport

primary: uses energy stored in ATP secondary: uses the energy stored in an electrochemical gradient

lysosomes (what/function & key feature)

site where macromolecules are broken down into their individual parts (AKA acid hydrolysis - hydrolysis = reverse of condensation) key feature: occurs efficiently under ACIDIC conditions - have a very low pH compared to rest of the cell & what's generally found outside of the cell

IMP PRINCIPLE 3: the electrochemical gradient

sodium has 2 features in water: an object & has a charge, which can be separated into separate identities: 1. number of objects = chemical gradient 2. charge differential = electro gradient gradient = differential across a membrane 2 forces at work: 1. chemical: if more of an object on one side of membrane than other: force through diffusion if can pass through to equalize the number of objects on both side of the gradient 2. electro: difference in charge - force that drives the charged particle across the membrane to balance charge electrochemical gradient can be maintained in way where it's like a battery: collected up & can dissipate it! can work additively or against each other

the relationship between X-Y is also important for enzymes

structure-function

X-ray crystallography

technique used to study the location of atoms in an enzyme or a enzyme substrate complex HOW •Purify protein (have high concentration of protein & get rid of everything unnecessary) •Many proteins will form a crystal •If have a pure crystal, can get a regular structure (like DNaseI ex on L) •Can take crystal & put in x-ray beam •When x-rays go through the crystal, hit individual electrons & get scattered •Pattern of scattering, bc of regular form over & over, the way the protein is sitting together in crystal, generates a characteristic diffraction pattern (repeating dots in middle picture) •From pattern of dots, can predict / make a density of where the electrons are in the particular individual repeating structure (the protein) (R image = electron density map of protein bound to pNP) •See that where "mountains" are = where electrons tend to be, can superimpose chemical structure of pNP onto the map & see where there's a carbon, there's not e-s and can see density in between where shared) •So from map, can impose known structure of a molecule / protein & generate a model of the molecule / protein! •Bottom image = protein interacting with a phosphate Can see / predict/ make model of where side chains are that'd be interacting with that phosphate when it's sitting inside the active site (so can be very informative in a variety of ways!)

changing activation energy is about changing X

the microenvironment (the context) Environment where chemical reaction occurs has an iron attached in there That particular iron has an affinity for binding to oxygen Hemoglobin has a similar thing together Something that can hold on to oxygen really wall Iron = covalently linked to a side chain protein itself (tyrosine) SO set of things / intermediates, step by step, happening that happen only because the substrate (peroxide) is inside the enzyme in the active site

how proteins & other macromolecules get between organelles ("doors")

the nuclear lumen is connected with the cytoplasm by nuclear pores a pore = opening between cytoplasm & nucleus, in this case, or other organelles selective pore allows certain passage of larger molecules through when importin bound to protein gets to pore, gets permission to enter, pulls protein (ex: histone) into the organelle (ex: nucleus) nuclear pore complex = important passage!! (how pass between specific sub-cellular localizations) - regulates passage of larger molecules through pore: import of proteins from cytoplasm, export of RNA to cytoplasm

tree of life: prokaryotes vs eukaryotes

tree of life: shows many types of organisms placed based on relatedness find much more variation in prokaryotes than eukaryotes prokaryotes = smaller cells (~10-100x smaller than eukaryotes), lack internal membrane systems (no nucleus / organelles), no histones - nucleoid eukaryotes include things like plants, animals, fungi, & protists

(t/f) substrates actually bind to the enzyme in the active site

true active site = where substrate touches the enzyme active site matches in shape to the substrate! (lock & key model) ("snap" together) shape of overall enzyme can change during the reaction, but the initial binding to the active site with the substrate is a matching together of 3D shapes! 4 active sites in catalase active site = place where actual complex (part of the substrate being inside an active site) that is critical for lowering the activation energy & accelerating reaction rate often talk about noncovalent bonds with enzymes, but sometimes (transiently) covalent bonds released again (case in catalase - intermediate where covalent bond between iron in active site & the oxygen) (or) An actual complex- relevant part of substrate is inside active site and often forms bonds with enzyme (non-covalent and sometimes -transiently-covalent)

enzyme catalyzed vs uncatalyzed reactions

use ∆G to determine if reaction is spontaneous or non Q: if see substrate & product beginning and end, what happened to ∆G? A: it's negative! so this reaction is spontaneous, and exergonic (so in principle, this reaction would occur from energetics standpoint - more energy come out to do work than what went in) *whether or not reaction happens is an entirely different question (e.g. wood burning is favorable, but needs / requires something else to start burning - can't burn on its own) (reason for this = activation energy!) *NOTE: free energy change (∆G) stays the same regardless of how hard you "push" (regardless of whether or not enzyme is present)